S. Figure on protein expression by cell type G vs P
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties
Endothelial cells
## Using CANARY, pt_ID as id variables

## Protein p.value FDR_corrected
## 1 144Nd_HLA-ABC 0.1714286 0.7619048
## 2 145Nd_CD31 0.4761905 0.7619048
## 3 146Nd_Thioredoxin 0.3523810 0.7619048
## 4 147Sm_b-CAT 0.4761905 0.7619048
## 5 156Gd_Vimentin 1.0000000 1.0000000
## 6 158Gd_p-STAT3 0.7619048 0.8465608
## 7 160Gd_MDM2 0.6095238 0.7619048
## 8 161Dy_Cytokeratin 0.4761905 0.7619048
## 9 163Dy_TP63 0.6095238 0.7619048
## 10 174Yb_HLA-DR 0.1714286 0.7619048
Fibroblasts/Mesenchymal cells
## Using CANARY, pt_ID as id variables
## Warning in wilcox.test.default(c(0, 0.0958118253303701, 0.284162729407862, :
## cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(0.802649816095183, 0.215492384630114,
## 0.0605647943338007, : cannot compute exact p-value with ties

## Protein p.value FDR_corrected
## 1 141Pr_EpCAM 0.76190476 0.9142857
## 2 142Nd_ccasp3 0.91428571 0.9142857
## 3 155Gd_CD56 0.47619048 0.8571429
## 4 156Gd_Vimentin 0.91428571 0.9142857
## 5 158Gd_p-STAT3 0.11428571 0.5142857
## 6 160Gd_MDM2 0.19945761 0.5983728
## 7 163Dy_TP63 0.47619048 0.8571429
## 8 170Yb_CD3 0.91406196 0.9142857
## 9 174Yb_HLA-DR 0.03809524 0.3428571
Immune cells
## Using CANARY, pt_ID as id variables
## Warning in wilcox.test.default(c(3.06708656196431, 0.066910551904235,
## 3.04431780411568, : cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(0.202586121632867, 0.0645635010399363, : cannot
## compute exact p-value with ties
## Warning in wilcox.test.default(c(0.501727573634015, 0.130067040154415,
## 0.712432219756351, : cannot compute exact p-value with ties

## Protein p.value FDR_corrected
## 1 144Nd_HLA-ABC 0.1055017 0.8571429
## 2 154Sm_CD45 0.4761905 0.9523810
## 3 156Gd_Vimentin 0.4761905 0.9523810
## 4 158Gd_p-STAT3 0.7619048 0.9523810
## 5 159Tb_CD4 0.9140620 1.0000000
## 6 163Dy_TP63 0.6095238 0.9523810
## 7 166Er_CD44 1.0000000 1.0000000
## 8 170Yb_CD3 0.7619048 0.9523810
## 9 171Yb_CD11b 0.3314247 0.9523810
## 10 174Yb_HLA-DR 0.1714286 0.8571429
CD8 T cells
## Using CANARY, pt_ID as id variables

## Protein p.value FDR_corrected
## 1 144Nd_HLA-ABC 0.03174603 0.2539683
## 2 154Sm_CD45 0.90476190 0.9047619
## 3 156Gd_Vimentin 0.55555556 0.8344671
## 4 163Dy_TP63 0.19047619 0.5079365
## 5 166Er_CD44 0.73015873 0.8344671
## 6 168Er_CD8 0.55555556 0.8344671
## 7 170Yb_CD3 0.73015873 0.8344671
## 8 174Yb_HLA-DR 0.11111111 0.4444444
CD4 T cells
## Using CANARY, pt_ID as id variables
## Warning in wilcox.test.default(c(0, 0.0561621657336121, 0, 0), c(0, 0,
## 1.50456532271426, : cannot compute exact p-value with ties

## Protein p.value FDR_corrected
## 1 144Nd_HLA-ABC 0.6095238 0.9142857
## 2 154Sm_CD45 0.3523810 0.7928571
## 3 156Gd_Vimentin 0.2571429 0.7714286
## 4 159Tb_CD4 0.6095238 0.9142857
## 5 163Dy_TP63 0.7619048 0.9795918
## 6 166Er_CD44 0.1714286 0.7714286
## 7 169Tm_CD24 1.0000000 1.0000000
## 8 170Yb_CD3 0.2571429 0.7714286
## 9 174Yb_HLA-DR 0.9142857 1.0000000
Myeloid cells
## Using CANARY, pt_ID as id variables
## Warning in wilcox.test.default(c(3.30075534359615, 0.0972935332589382,
## 3.31354462816258, : cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(1.62386202915046, 0.717296683223608,
## 2.44717234480325, : cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(0.748820669157824, 0.123253874437529,
## 1.67192224879611, : cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(0.63662474810693, 0.0913139040611759,
## 1.20841095112529, : cannot compute exact p-value with ties

## Protein p.value FDR_corrected
## 1 144Nd_HLA-ABC 0.1645218 0.9523810
## 2 145Nd_CD31 0.4541743 0.9523810
## 3 146Nd_Thioredoxin 0.5929097 0.9846154
## 4 154Sm_CD45 0.4761905 0.9523810
## 5 156Gd_Vimentin 0.4761905 0.9523810
## 6 158Gd_p-STAT3 0.3523810 0.9523810
## 7 159Tb_CD4 0.7461278 0.9846154
## 8 160Gd_MDM2 0.9142857 0.9846154
## 9 163Dy_TP63 1.0000000 1.0000000
## 10 166Er_CD44 0.9142857 0.9846154
## 11 171Yb_CD11b 0.4761905 0.9523810
## 12 172Yb_p-S6 0.9142857 0.9846154
## 13 174Yb_HLA-DR 0.2571429 0.9523810
## 14 175Lu_PD-L1 0.7619048 0.9846154
Epithelial cells
## Using CANARY, pt_ID as id variables
## Warning in wilcox.test.default(c(2.33079293987923, 0.0582644008491126,
## 1.75087785796523, : cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(1.63156525887895, 0.322305842850225,
## 1.32203451663395, : cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(1.13653172069154, 0.0527562183492093,
## 1.50292979733778, : cannot compute exact p-value with ties

## Protein p.value FDR_corrected
## 1 141Pr_EpCAM 0.11428571 0.4114286
## 2 142Nd_ccasp3 0.35238095 0.5714286
## 3 144Nd_HLA-ABC 0.16452182 0.4408163
## 4 147Sm_b-CAT 0.17142857 0.4408163
## 5 148Nd_HER2 0.03809524 0.4114286
## 6 151Eu_TTF1 0.09898793 0.4114286
## 7 154Sm_CD45 0.47619048 0.5714286
## 8 155Gd_CD56 0.76190476 0.8067227
## 9 156Gd_Vimentin 0.47619048 0.5714286
## 10 158Gd_p-STAT3 0.35238095 0.5714286
## 11 160Gd_MDM2 0.91428571 0.9142857
## 12 161Dy_Cytokeratin 0.11428571 0.4114286
## 13 162Dy_MET 0.25714286 0.5142857
## 14 163Dy_TP63 0.47619048 0.5714286
## 15 164Dy_CK7 0.47619048 0.5714286
## 16 165Ho_EGFR 0.10550173 0.4114286
## 17 170Yb_CD3 0.60952381 0.6857143
## 18 174Yb_HLA-DR 0.25714286 0.5142857